The protein-protein interaction network of eyestalk, Y-organ and hepatopancreas in Chinese mitten crab Eriocheir sinensis

BMC Systems Biology

Jinsheng Sun²  Xuyun Geng²  Yichen Liu¹  Yichen Zhang¹  Bin Wang¹  Zheng Zeng¹  Tong Hao¹ 

[1] Tianjin Key Laboratory of Animal and Plant Resistance/College of Life Science, Tianjin Normal University, Tianjin 300387, P.R. China;Tianjin Aquatic Animal Infectious Disease Control and Prevention Center, Tianjin 300221, P.R. China

关键词: Evolution path;    Signal transduction;    Network integration;    Chinese mitten crab;    Eriocheir sinensis;   

Others  :  866592
DOI  :  10.1186/1752-0509-8-39

 received in 2014-01-11, accepted in 2014-03-21,  发布年份 2014

【 摘 要 】

Background

The protein-protein interaction network (PIN) is an effective information tool for understanding the complex biological processes inside the cell and solving many biological problems such as signaling pathway identification and prediction of protein functions. Eriocheir sinensis is a highly-commercial aquaculture species with an unclear proteome background which hinders the construction and development of PIN for E. sinensis. However, in recent years, the development of next-generation deep-sequencing techniques makes it possible to get high throughput data of E. sinensis tanscriptome and subsequently obtain a systematic overview of the protein-protein interaction system.

Results

In this work we sequenced the transcriptional RNA of eyestalk, Y-organ and hepatopancreas in E. sinensis and generated a PIN of E. sinensis which included 3,223 proteins and 35,787 interactions. Each protein-protein interaction in the network was scored according to the homology and genetic relationship. The signaling sub-network, representing the signal transduction pathways in E. sinensis, was extracted from the global network, which depicted a global view of the signaling systems in E. sinensis. Seven basic signal transduction pathways were identified in E. sinensis. By investigating the evolution paths of the seven pathways, we found that these pathways got mature in different evolutionary stages. Moreover, the functions of unclassified proteins and unigenes in the PIN of E. sinensis were predicted. Specifically, the functions of 549 unclassified proteins related to 864 unclassified unigenes were assigned, which respectively covered 76% and 73% of all the unclassified proteins and unigenes in the network.

Conclusions

The PIN generated in this work is the first large-scale PIN of aquatic crustacean, thereby providing a paradigmatic blueprint of the aquatic crustacean interactome. Signaling sub-network extracted from the global PIN depicts the interaction of different signaling proteins and the evolutionary paths of the identified signal transduction pathways. Furthermore, the function assignment of unclassified proteins based on the PIN offers a new reference in protein function exploration. More importantly, the construction of the E. sinensis PIN provides necessary experience for the exploration of PINs in other aquatic crustacean species.

【 授权许可】

   
2014 Hao et al.; licensee BioMed Central Ltd.

【 图 表 】

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